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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
* DESCRIPTION: WFA C++ Sample-Code
*/
#include <iostream>
#include <string>
#include "bindings/cpp/WFAligner.hpp"
using namespace std;
using namespace wfa;
int main(int argc,char* argv[]) {
// Patter & Text
string pattern = "TCTTTACTCGCGCGTTGGAGAAATACAATAGT";
string text = "TCTATACTGCGCGTTTGGAGAAATAAAATAGT";
// Create a WFAligner
WFAlignerGapAffine aligner(4,6,2,WFAligner::Alignment,WFAligner::MemoryHigh);
// Align
aligner.alignEnd2End(pattern,text);
cout << "WFA-Alignment returns score " << aligner.getAlignmentScore() << endl;
// Print CIGAR
string cigar = aligner.getAlignmentCigar();
cout << "PATTERN: " << pattern << endl;
cout << "TEXT: " << text << endl;
cout << "CIGAR: " << cigar << endl;
}
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